I can confirm from experience that the TruSeq RNA Access (now RNA Exome) performs really well with degraded FFPE material and generates consistent, high quality libraries from FFPE samples even with low DV200 scores. As far as multiplexing goes the kit has options for a Set A and Set B index kit which gives a total of 24 unique libraries for pooling and sequencing. I don't have any experience in using other index possibilities with the kit (like dual indexing) for a greater amount of uniquely barcoded libraries. It may be worth contacting Illumina to see if a solution exists.

A quick look on the product page for the TruSeq RNA Exome kit states that multiplex options are 24 single index or up to 96 combinatorial dual indexes. This seems like it would meet your criteria for your 48 samples multiplexing.